Profile: The Kilifi Health and Demographic Surveillance System (KHDSS)

Validation of a Swahili version of the World Health Organization 5-item well-being index among adults living with HIV and epilepsy in rural coastal Kenya

OBJECTIVE

The purpose of this study was to evaluate the psychometric properties of the World Health Organization's five item well-being index (WHO-5) when administered to adults living with HIV or epilepsy in a rural setting at the coast of Kenya.

METHODS

A case control study design was conducted among 230 adults aged 18-50 years, who comprised 147 cases (63 living with epilepsy and 84 living with HIV) and 83 healthy controls. The participants were administered to a face-to-face interview during which they completed the Swahili version of WHO-5 well-being index, the Major Depression Inventory (MDI) and responded to some items on their socio-demographic characteristics. Analysis to assess internal consistency, construct validity, discriminant validity, and convergent validity of the Swahili version of WHO-5 well-being index was conducted. A multivariate regression was carried out to assess the association between psychological wellbeing (assessed using Swahili version of WHO-5 well-being index) and having a chronic illness (HIV or epilepsy).

RESULTS

The Swahili version of WHO-5 well-being index demonstrated good internal consistency with Cronbach alpha ranges of 0.86-0.88 among the three study groups. The tool had good discriminant validity. A one factor structure of the tool was obtained from confirmatory factor analysis (overall Comparative Fit Index = 1.00, Tuckler Lewis Index = 1.01, Root Mean Square of Error Approximation = 0.00). Living with HIV or epilepsy in comparison to being a healthy control was significantly associated with greater odds of having sub-optimal psychological wellbeing.

CONCLUSION

Our findings demonstrate that the Swahili version of WHO-5 well-being index has good psychometric properties and is appropriate for use to evaluate psychological well-being among adults living with chronic conditions such as HIV or epilepsy from a rural low resource setting in Kenya. Given its brevity and ease of use, the Swahili version of WHO-5 well-being index could potentially be used by lay workers and other paraprofessional to monitor psychological well-being among chronically ill adults in resource poor settings.

Suicide in a rural area of coastal Kenya

BACKGROUND

Suicide accounts for approximately 1.4% of deaths globally and is the 15th leading cause of death overall. There are no reliable data on the epidemiology of completed suicide in rural areas of many developing countries, yet suicide is an indicator of the sustainable development goals on health.

METHODS

Using data collected between 2008 and 2016 from the Kilifi Health and Demographic Surveillance System in rural Kenya, we retrospectively determined the incidence rate and risk factors for completed suicide.

RESULTS

During the period, 104 people died by suicide, contributing to 0.78% (95% CI = 0.74-1.10) of all deaths. The mean annual incidence rate of suicide was 4.61 (95% CI = 3.80-5.58) per 100,000 person years of observation (pyo). The annual incidence rate for men was higher than that of women (IRR = 3.05, 95% CI = 1.98-4.70, p < 0.001) and it increased with age (IRR = 2.73, 95% CI = 2.30-3.24, p < 0.001). People aged > 64 years had the highest mean incidence rate of 18.58 (95% CI = 11.99-28.80) per 100,000 pyo. Completed suicide was associated with age, being male, and living in a house whose wall is made of scrap material, which is a proxy marker of extreme poverty in this region (OR = 5.5, 95% CI = 4.0-7.0, p = 0.02). Most cases (76%) completed suicide by hanging themselves. Spatial heterogeneity of rates of suicides was observed across the enumeration zones of the KHDSS.

CONCLUSIONS

Suicide is common in this area, but the incidence of completed suicide in rural Kenya may be an underestimate of the true burden. Like in other studies, suicide was associated with older age, being male and poverty, but other medical and neuropsychiatric risk factors should be investigated in future studies.

Cognition, mood and quality-of-life outcomes among low literacy adults living with epilepsy in rural Kenya: A preliminary study

Epilepsy is frequently associated with neurocognitive impairments, mental health, and psychosocial problems but these are rarely documented in low- and middle-income countries. The aim of this study was to examine the neurocognitive outcomes, depressive symptoms, and psychosocial adjustments of people with epilepsy (PWE) in Kilifi, Kenya. We evaluated the impact of these outcomes on health-related quality of life. Self-report, interviewer-administered measures of depression (Major Depression Inventory) and quality of life (RAND SF-36) were administered to 63 PWE and 83 community controls. Neurocognitive functioning was assessed using Raven's Standard Progressive Matrices, Digit Span, and Contingency Naming Test. The results show that PWE have poorer scores for executive function, working memory, intelligence quotient (IQ), depression, and quality of life than controls. Twenty-seven (27%) of PWE had depressive symptoms, which was significantly greater than in controls (6%); P < 0.001. Quality-of-life scores were significantly lower in PWE with depressive symptoms than in those without depressive symptoms (Mean QoL scores (standard deviation (SD)): 46.43 (13.27) versus 64.18 (17.69); P = 0.01. On adjusted linear regression models, depression affected total quality-of-life scores (P = 0.07) as well as individual health indicator domains touching on pain (P = 0.04), lethargy/fatigue (P = 0.01), and emotional well-being (P = 0.02). Our results show that epilepsy is associated with a significant burden of mental health and neurocognitive impairments in the community; however, community-based studies are needed to provide precise estimates of these disorders.

Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study

BACKGROUND

Human genetic factors are important determinants of malaria risk. We investigated associations between multiple candidate polymorphisms-many related to the structure or function of red blood cells-and risk for severe Plasmodium falciparum malaria and its specific phenotypes, including cerebral malaria, severe malaria anaemia, and respiratory distress.

METHODS

We did a case-control study in Kilifi County, Kenya. We recruited as cases children presenting with severe malaria to the high-dependency ward of Kilifi County Hospital. We included as controls infants born in the local community between Aug 1, 2006, and Sept 30, 2010, who were part of a genetics study. We tested for associations between a range of candidate malaria-protective genes and risk for severe malaria and its specific phenotypes. We used a permutation approach to account for multiple comparisons between polymorphisms and severe malaria. We judged p values less than 0·005 significant for the primary analysis of the association between candidate genes and severe malaria.

FINDINGS

Between June 11, 1995, and June 12, 2008, 2244 children with severe malaria were recruited to the study, and 3949 infants were included as controls. Overall, 263 (12%) of 2244 children with severe malaria died in hospital, including 196 (16%) of 1233 with cerebral malaria. We investigated 121 polymorphisms in 70 candidate severe malaria-associated genes. We found significant associations between risk for severe malaria overall and polymorphisms in 15 genes or locations, of which most were related to red blood cells: ABO, ATP2B4, ARL14, CD40LG, FREM3, INPP4B, G6PD, HBA (both HBA1 and HBA2), HBB, IL10, LPHN2 (also known as ADGRL2), LOC727982, RPS6KL1, CAND1, and GNAS. Combined, these genetic associations accounted for 5·2% of the variance in risk for developing severe malaria among individuals in the general population. We confirmed established associations between severe malaria and sickle-cell trait (odds ratio [OR] 0·15, 95% CI 0·11-0·20; p=2·61 × 10-58), blood group O (0·74, 0·66-0·82; p=6·26 × 10-8), and -α3·7-thalassaemia (0·83, 0·76-0·90; p=2·06 × 10-6). We also found strong associations between overall risk of severe malaria and polymorphisms in both ATP2B4 (OR 0·76, 95% CI 0·63-0·92; p=0·001) and FREM3 (0·64, 0·53-0·79; p=3·18 × 10-14). The association with FREM3 could be accounted for by linkage disequilibrium with a complex structural mutation within the glycophorin gene region (comprising GYPA, GYPB, and GYPE) that encodes for the rare Dantu blood group antigen. Heterozygosity for Dantu was associated with risk for severe malaria (OR 0·57, 95% CI 0·49-0·68; p=3·22 × 10-11), as was homozygosity (0·26, 0·11-0·62; p=0·002).

INTERPRETATION

Both ATP2B4 and the Dantu blood group antigen are associated with the structure and function of red blood cells. ATP2B4 codes for plasma membrane calcium-transporting ATPase 4 (the major calcium pump on red blood cells) and the glycophorins are ligands for parasites to invade red blood cells. Future work should aim at uncovering the mechanisms by which these polymorphisms can result in severe malaria protection and investigate the implications of these associations for wider health.

FUNDING

Wellcome Trust, UK Medical Research Council, European Union, and Foundation for the National Institutes of Health as part of the Bill & Melinda Gates Grand Challenges in Global Health Initiative.

Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya: baseline epidemiological observations

Background: Endemic and seasonally recurring respiratory viruses are a major cause of disease and death globally. The burden is particularly severe in developing countries. Improved understanding of the source of infection, pathways of spread and persistence in communities would be of benefit in devising intervention strategies. Methods: We report epidemiological data obtained through surveillance of respiratory viruses at nine outpatient health facilities within the Kilifi Health and Demographic Surveillance System, Kilifi County, coastal Kenya, between January and December 2016. Nasopharyngeal swabs were collected from individuals of all ages presenting with acute respiratory infection (ARI) symptoms (up to 15 swabs per week per facility) and screened for 15 respiratory viruses using real-time PCR. Paediatric inpatient surveillance at Kilifi County Hospital for respiratory viruses provided comparative data. Results: Over the year, 5,647 participants were sampled, of which 3,029 (53.7%) were aged <5 years. At least one target respiratory virus was detected in 2,380 (42.2%) of the samples; the most common being rhinovirus 18.6% (1,050), influenza virus 6.9% (390), coronavirus 6.8% (387), parainfluenza virus 6.6% (371), respiratory syncytial virus (RSV) 3.9% (219) and adenovirus 2.7% (155). Virus detections were higher among <5-year-olds compared to older children and adults (50.3% vs 32.7%, respectively; χ 2(1) =177.3, P=0.0001). Frequency of viruses did not differ significantly by facility (χ 2(8) =13.38, P=0.072). However, prevalence was significantly higher among inpatients than outpatients in <5-year-olds for RSV (22.1% vs 6.0%; χ 2(1) = 159.4, P=0.0001), and adenovirus (12.4% vs 4.4%, χ 2(1) =56.6, P=0.0001). Conclusions: Respiratory virus infections are common amongst ARI outpatients in this coastal Kenya setting, particularly in young children. Rhinovirus predominance warrants further studies on the health and socio-economic implications. RSV and adenovirus were more commonly associated with severe disease. Further analysis will explore epidemiological transmission patterns with the addition of virus sequence data.

Reliability and validity of the World Health Organization reading standards for paediatric chest radiographs used in the field in an impact study of Pneumococcal Conjugate Vaccine in Kilifi, Kenya

BACKGROUND

Radiologically-confirmed pneumonia (RCP) is a specific end-point used in trials of Pneumococcal Conjugate Vaccine (PCV) to estimate vaccine efficacy. However, chest radiograph (CXR) interpretation varies within and between readers. We measured the repeatability and reliability of paediatric CXR interpretation using percent agreement and Cohen's Kappa and the validity of field readings against expert review in a study of the impact of PCV on pneumonia.

METHODS

CXRs were obtained from 2716 children admitted between 2006 and 2014 to Kilifi County Hospital, Kilifi, Kenya, with clinically-defined severe or very-severe pneumonia. Five clinicians and radiologists attended a three-day training course on CXR interpretation using a WHO standard. All CXRs were read once by two local primary readers. Discordant readings and 13% of concordant readings were arbitrated by a panel of three expert radiologists. To assess repeatability, a 5% median random sample was presented twice. Sensitivity and specificity of the primary readers' interpretations was estimated against the 'gold-standard' of the arbitrators' results.

RESULTS

Of 2716 CXRs, 2 were uninterpretable and 159 were evaluated twice. The percent agreement and Kappa for RCP were 89% and 0.68 and ranged between 84-97% and 0.19-0.68, respectively, for all pathological findings. Intra-observer repeatability was similar to inter-observer reliability. Sensitivities of the primary readers to detect RCP were 69% and 73%; specificities were 96% and 95%.

CONCLUSION

Intra- and inter-observer agreements on interpretations of radiologically-confirmed pneumonia are fair to good. Reasonable sensitivity and high specificity make radiologically-confirmed pneumonia, determined in the field, a suitable measure of relative vaccine effectiveness.

Impact of viral upper respiratory tract infection on the concentration of nasopharyngeal pneumococcal carriage among Kenyan children

Viral upper respiratory tract infection (URTI) predisposes to bacterial pneumonia possibly by facilitating growth of bacteria such as Streptococcus pneumoniae colonising the nasopharynx. We investigated whether viral URTI is temporally associated with an increase in nasopharyngeal pneumococcal concentration. Episodes of symptomatic RSV or rhinovirus URTI among children <5 years were identified from a longitudinal household study in rural Kenya. lytA and alu PCR were performed on nasopharyngeal samples collected twice-weekly, to measure the pneumococcal concentration adjusted for the concentration of human DNA present. Pneumococcal concentration increased with a fold-change of 3.80 (95%CI 1.95-7.40), with acquisition of RSV or rhinovirus, during 51 URTI episodes among 42 children. In repeated swabs from the baseline period, in the two weeks before URTI developed, within-episode variation was broad; within +/-112-fold range of the geometric mean. We observed only a small increase in nasopharyngeal pneumococcal concentration during RSV or rhinovirus URTI, relative to natural variation. Other factors, such as host response to viral infection, may be more important than nasopharyngeal pneumococcal concentration in determining risk of invasive disease.

Implications for paediatric shock management in resource-limited settings: a perspective from the FEAST trial

BACKGROUND

Although the African "Fluid Expansion as Supportive therapy" (FEAST) trial showed fluid resuscitation was harmful in children with severe febrile illness managed in resource-limited hospitals, the most recent evidence reviewed World Health Organization (WHO) guidelines continue to recommend fluid boluses in children with shock according to WHO criteria "WHO shock", arguing that the numbers included in the FEAST trial were too small to provide reasonable certainty.

METHODS

We re-analysed the FEAST trial results for all international definitions for paediatric shock including hypotensive (or decompensated shock) and the WHO criteria. In addition, we examined the clinical relevance of the WHO criteria to published and unpublished observational studies reporting shock in resource-limited settings.

RESULTS

We established that hypotension was rare in children with severe febrile illness complicating only 29/3170 trial participants (0.9%). We confirmed that fluid boluses were harmful irrespective of the definitions of shock including the very small number with WHO shock (n = 65). In this subgroup 48% of bolus recipients died at 48 h compared to 20% of the non-bolus control group, an increased absolute risk of 28%, but translating to an increased relative risk of 240% (p = 0.07 (two-sided Fisher's exact test)). Examining studies describing the prevalence of the stringent WHO shock criteria in children presenting to hospital we found this was rare (~ 0.1%) and in these children mortality was very high (41.5-100%).

CONCLUSIONS

The updated WHO guidelines continue to recommend boluses for a very limited number of children presenting at hospital with the strict definition of WHO shock. Nevertheless, the 3% increased mortality from boluses seen across FEAST trial participants would also include this subgroup of children receiving boluses. Recommendations aiming to differentiate WHO shock from other definitions will invariably lead to "slippage" at the bedside, with the potential of exposing a wider group of children to the harm of fluid-bolus therapy.

Two complement receptor one alleles have opposing associations with cerebral malaria and interact with α+thalassaemia

Malaria has been a major driving force in the evolution of the human genome. In sub-Saharan African populations, two neighbouring polymorphisms in the Complement Receptor One (CR1) gene, named Sl2 and McCb, occur at high frequencies, consistent with selection by malaria. Previous studies have been inconclusive. Using a large case-control study of severe malaria in Kenyan children and statistical models adjusted for confounders, we estimate the relationship between Sl2 and McCb and malaria phenotypes, and find they have opposing associations. The Sl2 polymorphism is associated with markedly reduced odds of cerebral malaria and death, while the McCb polymorphism is associated with increased odds of cerebral malaria. We also identify an apparent interaction between Sl2 and α+thalassaemia, with the protective association of Sl2 greatest in children with normal α-globin. The complex relationship between these three mutations may explain previous conflicting findings, highlighting the importance of considering genetic interactions in disease-association studies.

Ethical considerations in Controlled Human Malaria Infection studies in low resource settings: Experiences and perceptions of study participants in a malaria Challenge study in Kenya

Background: The range and amount of volunteer infection studies, known as Controlled Human Infection Model (CHMI) studies, in Low-Middle Income Countries (LMICs) is increasing with rapid technological advancement, world-class laboratory facilities and increasing capacity development initiatives. However, the ethical issues these studies present in LMICs have not been empirically studied. We present findings of a descriptive social science study nested within a malaria volunteer infection study, on-going at the time of writing, at the KEMRI-Wellcome Trust Research Programme (KWTRP) on the Kenyan Coast. Methods: The study included non-participant observations, five group discussions with more than half of the CHMI study participants, two in-depth interviews with study team members, and an exit questionnaire administered to the participants. Results: Participants understood the key elements of the study, including that they would be deliberately infected with malaria parasites and may get malaria as a result, there would be regular blood draws, and they would spend up to 24 days in a residence facility away from their homes. The greatest motivation for participation was the monetary compensation of 20 USD per overnight stay given as a lump-sum at the end of their residency stay.  Also appreciated were the health screening tests prior to enrolment and the positive relations with the study team. Concerns raised included the amount and regularity of blood draws experienced, and concerns that this type of research may feed into on-going rumours about research generally. Conclusion: With the increasing range and number of CHMI studies being conducted in LMICs, current ethical guidance for more than minimal risk studies is inadequate. This study highlights some of the ethical issues that could emerge in these settings, emphasizing the heavy responsibility placed on research review and regulatory systems, researchers and funders, as well as the importance of carefully tailored community engagement and consent processes.

Prevalence and correlates of home delivery amongst HIV-infected women attending care at a rural public health facility in Coastal Kenya

BACKGROUND

Home delivery, referring to pregnant women giving birth in the absence of a skilled birth attendant, is a significant contributor to maternal mortality, and is encouragingly reported to be on a decline in the general population in resource limited settings. However, much less is known about home delivery amongst HIV-infected women in sub-Saharan Africa (sSA). We described the prevalence and correlates of home delivery among HIV-infected women attending care at a rural public health facility in Kilifi, Coastal Kenya.

METHODS

A cross-sectional design using mixed methods was used. Quantitative data were collected using interviewer-administered questionnaires from HIV-infected women with a recent pregnancy (within 5 years, n = 425), whilst qualitative data were collected using focused group discussions (FGD, n = 5). Data were analysed using logistic regression and a thematic framework approach respectively.

RESULTS

Overall, 108 (25.4%, [95% CI: 21.3-29.8]) participants delivered at home. Correlates of home delivery included lack of formal education (aOR 12.4 [95% CI: 3.4-46.0], p<0.001), history of a previous home delivery (2.7 [95% CI:1.2-6.0], p = 0.019) and being on highly active antiretroviral therapy (HAART, 0.4 [95% CI:0.2-0.8], p = 0.006).Despite a strong endorsement against home delivery, major thematic challenges included consumer-associated barriers, health care provider associated barriers and structural barriers.

CONCLUSION

A quarter of HIV-infected women delivered at home, which is comparable to estimates reported from the general population in this rural setting, and much lower than estimates from other sSA settings. A tailored package of care targeting women with no formal education and with a history of a previous home delivery, coupled with interventions towards scaling up HAART and improving the quality of maternal care in HIV-infected women may positively contribute to a decline in home delivery and subsequent maternal mortality in this setting.

Prevalence, risk factors and behavioural and emotional comorbidity of acute seizures in young Kenyan children: a population-based study

BACKGROUND

Acute symptomatic seizures and febrile seizures are common in children admitted to hospitals in Africa and may be markers of brain dysfunction. They may be associated with behavioural and emotional problems, but there are no published community-based studies in Africa.

METHODS

We screened 7047 children aged 1-6 years (randomly sampled from 50,000 in the community) for seizures (using seven questions) and invited those who screened positive and a proportion of negatives for a clinical assessment. Risk factors were identified using a parental questionnaire. Behavioural and emotional problems were examined using the Child Behaviour Checklist (CBCL) in 3273 children randomly selected from 7047. Generalised linear models with appropriate link functions were used to determine risk factors and associations between behavioural or emotional problems and acute seizures. Sobel-Goodman mediation tests were used to investigate if the association between acute seizures and CBCL scores was mediated by co-diagnosis of epilepsy.

RESULTS

Acute seizures were identified in 429 (6.1%) preschool children: 3.2% (95% confidence interval CI: 2.9-3.5%) for symptomatic seizures, and 2.9% (95% CI: 2.6-3.3%) for febrile seizures. Risk factors for acute seizures included family history of febrile seizures (odds ratio OR = 3.19; 95% CI: 2.03-5.01) and previous hospitalisation (OR = 6.65; 95% CI: 4.60-9.63). Total CBCL problems occurred more frequently in children with acute seizures (27%; 95% CI: 21-34%) than for those without seizures (11%; 95% CI: 11-12%; chi-squared p ≤ 0.001). Acute seizures were associated with total CBCL problems (adjusted risk ratio (aRR) = 1.92; 95% CI: 1.34-2.77), externalising problems (aRR = 1.82; 95% CI: 1.21-2.75) and internalising problems (aRR = 1.57; 95% CI: 1.22-2.02), with the proportion of the comorbidity mediated by a co-diagnosis of epilepsy being small (15.3%; 95% CI: 4.5-34.9%). Risk factors for this comorbidity included family history of febrile seizures (risk ratio (RR) = 3.36; 95% CI: 1.34-8.41), repetitive acute seizures (β = 0.36; 95% CI: 0.15-0.57) and focal acute seizures (RR = 1.80; 95% CI: 1.05-3.08).

CONCLUSIONS

Acute seizures are common in preschool children in this area and are associated with behavioural and emotional problems. Both conditions should be assessed and addressed in children.

The clinical epidemiology of sickle cell anemia In Africa

Sickle cell anemia (SCA) is the commonest severe monogenic disorders of humans. The disease has been highly characterized in high‐income countries but not in sub‐Saharan Africa where SCA is most prevalent. We conducted a retrospective cohort study of all children 0–13 years admitted from within a defined study area to Kilifi County Hospital in Kenya over a five‐year period. Children were genotyped for SCA retrospectively and incidence rates calculated with reference to population data. Overall, 576 of 18,873 (3.1%) admissions had SCA of whom the majority (399; 69.3%) were previously undiagnosed. The incidence of all‐cause hospital admission was 57.2/100 person years of observation (PYO; 95%CI 52.6–62.1) in children with SCA and 3.7/100 PYO (95%CI 3.7–3.8) in those without SCA (IRR 15.3; 95%CI 14.1–16.6). Rates were higher for the majority of syndromic diagnoses at all ages beyond the neonatal period, being especially high for severe anemia (hemoglobin <50 g/L; IRR 58.8; 95%CI 50.3–68.7), stroke (IRR 486; 95%CI 68.4–3,450), bacteremia (IRR 23.4; 95%CI 17.4–31.4), and for bone (IRR 607; 95%CI 284–1,300), and joint (IRR 80.9; 95%CI 18.1–362) infections. The use of an algorithm based on just five clinical features would have identified approximately half of all SCA cases among hospital‐admitted children with a number needed to test to identify each affected patient of only fourteen. Our study illustrates the clinical epidemiology of SCA in a malaria‐endemic environment without specific interventions. The targeted testing of hospital‐admitted children using the Kilifi Algorithm provides a pragmatic approach to early diagnosis in high‐prevalence countries where newborn screening is unavailable.

Should Controls With Respiratory Symptoms Be Excluded From Case-Control Studies of Pneumonia Etiology? Reflections From the PERCH Study

Many pneumonia etiology case-control studies exclude controls with respiratory illness from enrollment or analyses. Herein we argue that selecting controls regardless of respiratory symptoms provides the least biased estimates of pneumonia etiology. We review 3 reasons investigators may choose to exclude controls with respiratory symptoms in light of epidemiologic principles of control selection and present data from the Pneumonia Etiology Research for Child Health (PERCH) study where relevant to assess their validity. We conclude that exclusion of controls with respiratory symptoms will result in biased estimates of etiology. Randomly selected community controls, with or without respiratory symptoms, as long as they do not meet the criteria for case-defining pneumonia, are most representative of the general population from which cases arose and the least subject to selection bias.

Perspectives on Underlying Factors for Unhealthy Diet and Sedentary Lifestyle of Adolescents at a Kenyan Coastal Setting

Unhealthy diet and physical inactivity are among the key modifiable risk factors for non-communicable diseases, such as diabetes and cardiovascular disease. Although such diseases often only appear in adulthood, these behaviors are typically initiated or reinforced already during adolescence. However, knowledge on underlying factors for adolescents' unhealthy dieting and physical inactivity in sub-Saharan Africa (SSA) is poor. We conducted in-depth interviews and focus group discussions to explore the perceptions of a diverse group of 78 young people of 10-19 years of age, which also included some adolescents living with HIV, as this is an emerging group in the HIV/AIDS epidemic in many parts of SSA. In addition, 10 stakeholders, such as teachers, clinicians, and staff from organizations at the Kenyan coast and seven young adult community representatives informed us on: (a) adolescents' unhealthy food choices and their forms of sedentary behavior; (b) predisposing factors; and (c) protective factors against unhealthy food choices and sedentary behavior of adolescents living in Kilifi County. The findings reveal that adolescents occasionally access nutritious foods, such as fruits, vegetables, and animal protein. However, there is a growing tendency to consume unbalanced diets with high intake of carbohydrates, oily foods, and consumption of sugar dense processed foods and drinks. Sports and domestic chores were found to be major sources of physical activity. Sedentary lifestyles characterized by a long-time sitting and chatting, watching sports games and movies were described. Adolescents living with HIV did not indicate any divergent perceptions from those of other adolescents relating to diet and physical activity, but mentioned health-related conditions, such as medication, asthma, and low body weight, as a risk factors for sedentary lifestyle. Using a Socio-Ecological model, our findings suggest that risk factors are numerous and interrelated, especially at intrapersonal, interpersonal, and community level. The negative influences at an intrapersonal level were as follows: body image concerns, attitudes and misconceptions, substance use behavior, and taste for unhealthy foods. In the interpersonal domain, household poverty and parenting practices that condone unhealthy habits were identified risk factors. Availability of affordable unhealthy foods, high prices for nutritious food, farming practices, gambling, and influx of transportation alternatives in the community were interrelated but also had relationships with intrapersonal and interpersonal risk factors. Modernization and poor implementation of policies were discussed as enabling factors especially by stakeholders from a societal perspective. Seasonality and farming practices, school attendance, community-based services, and regulations mitigating adolescents' engagement in gambling were identified as potential protective factors. Our findings provide a unique qualitative insight of the factors underlying adolescents' dietary and sedentary lifestyle and highlight the need for ecological intervention approaches to address these forms of health risk behavior in a rural African setting.

Variation in the effectiveness of insecticide treated nets against malaria and outdoor biting by vectors in Kilifi, Kenya

Background: Insecticide treated nets (ITNs) protect humans against bites from the Anopheles mosquito vectors that transmit malaria, thereby reducing malaria morbidity and mortality. It has been noted that ITN use leads to a switch from indoor to outdoor feeding among these vectors. It might be expected that outdoor feeding would undermine the effectiveness of ITNs that target indoors vectors, but data are limited. Methods: We linked homestead level geospatial data to clinical surveillance data at a primary healthcare facility in Kilifi County in order to map geographical heterogeneity in ITN effectiveness and observed vector feeding behaviour using landing catches and CDC light traps in six selected areas of varying ITN effectiveness. We quantified the interaction between mosquitoes and humans to evaluate whether outdoor vector biting is a potential explanation for the variation in ITN effectiveness. Results: We observed 37% and 46% visits associated with positive malaria slides among ITN users and non-ITN-users, respectively; ITN use was associated with 32% protection from malaria (crude OR = 0.68, 95% CI: 0.64, 0.73). We obtained significant modification of ITN effectiveness by geographical area (p=0.016), and identified significant hotspots using the spatial scan statistic. Majority of mosquitoes were caught outdoor (60%) and were of the An. funestus group (75%). The overall propensity to feed at times when most people are indoor was high; the vast majority of the Anopheles mosquitoes were caught at times when most people are indoor. Estimates for the proportion of human-mosquito contact between the first and last hour when most humans were indoor was consistently high, ranging from 0.83 to 1.00. Conclusion: Our data therefore do not support the hypothesis that outdoor biting limits the effectiveness of ITNs in our study area.

No Evidence that Knops Blood Group Polymorphisms Affect Complement Receptor 1 Clustering on Erythrocytes

Clustering of Complement Receptor 1 (CR1) in the erythrocyte membrane is important for immune-complex transfer and clearance. CR1 contains the Knops blood group antigens, including the antithetical pairs Swain-Langley 1 and 2 (Sl1 and Sl2) and McCoy a and b (McC^a and McC^b), whose functional effects are unknown. We tested the hypothesis that the Sl and McC polymorphisms might influence CR1 clustering on erythrocyte membranes. Blood samples from 125 healthy Kenyan children were analysed by immunofluorescence and confocal microscopy to determine CR1 cluster number and volume. In agreement with previous reports, CR1 cluster number and volume were positively associated with CR1 copy number (mean number of CR1 molecules per erythrocyte). Individuals with the McC^b/McC^b genotype had more clusters per cell than McC^a/McC^a individuals. However, this association was lost when the strong effect of CR1 copy number was included in the model. No association was observed between Sl genotype, sickle cell genotype, α+thalassaemia genotype, gender or age and CR1 cluster number or volume. Therefore, after correction for CR1 copy number, the Sl and McCoy polymorphisms did not influence erythrocyte CR1 clustering, and the effects of the Knops polymorphisms on CR1 function remains unknown.

Detecting Malaria Hotspots: A Comparison of Rapid Diagnostic Test, Microscopy, and Polymerase Chain Reaction

Background

Malaria control strategies need to respond to geographical hotspots of transmission. Detection of hotspots depends on the sensitivity of the diagnostic tool used.

Methods

We conducted cross-sectional surveys in 3 sites within Kilifi County, Kenya, that had variable transmission intensities. Rapid diagnostic test (RDT), microscopy, and polymerase chain reaction (PCR) were used to detect asymptomatic parasitemia, and hotspots were detected using the spatial scan statistic.

Results

Eight thousand five hundred eighty-one study participants were surveyed in 3 sites. There were statistically significant malaria hotspots by RDT, microscopy, and PCR for all sites except by microscopy in 1 low transmission site. Pooled data analysis of hotspots by PCR overlapped with hotspots by microscopy at a moderate setting but not at 2 lower transmission settings. However, variations in degree of overlap were noted when data were analyzed by year. Hotspots by RDT were predictive of PCR/microscopy at the moderate setting, but not at the 2 low transmission settings. We observed long-term stability of hotspots by PCR and microscopy but not RDT.

Conclusion

Malaria control programs may consider PCR testing to guide asymptomatic malaria hotspot detection once the prevalence of infection falls.

Psychometric evaluation of the Major Depression Inventory among young people living in Coastal Kenya

Background: The lack of reliable, valid and adequately standardized measures of mental illnesses in sub-Saharan Africa is a key challenge for epidemiological studies on mental health.  We evaluated the psychometric properties and feasibility of using a computerized version of the Major Depression Inventory (MDI) in an epidemiological study in rural Kenya.

Methods: We surveyed 1496 participants aged 13-24 years in Kilifi County, on the Kenyan coast. The MDI was administered using a computer-assisted system, available in three languages. Internal consistency was evaluated using both Cronbach’s alpha and the Omega Coefficient. Confirmatory factor analysis was performed to evaluate the factorial structure of the MDI.

Results:  Internal consistency using both Cronbach’s Alpha (α= 0.83) and the Omega Coefficient (0.82; 95% confidence interval 0.81- 0.83) was above acceptable thresholds. Confirmatory factor analysis indicated a good fit of the data to a unidimensional model of MDI (χ ² (33, N = 1409) = 178.52 p < 0.001, TLI = 0.947, CFI = 0.961, and Root Mean Square Error of Approximation, RMSEA = .056), and this was confirmed using Item Response Models (Loevinger’s H coefficient 0.38) that proved the MDI was a unidimensional scale. Equivalence evaluation indicated invariance across sex and age groups. In our population, 3.6% of the youth presented with scores suggesting major depression using the ICD-10 scoring algorithm, and 8.7% presented with total scores indicating presence of depression (mild, moderate or severe).  Females and older youth were at the highest risk of depression.

Conclusions: The MDI has good psychometric properties.  Given its brevity, relative ease of usage and ability to identify at-risk youth, it may be useful for epidemiological studies of depression in Africa.  Studies to establish clinical thresholds for depression are recommended. The high prevalence of depressive symptoms suggests that depression may be an important public health problem in this population group.

Trends in bednet ownership and usage, and the effect of bednets on malaria hospitalization in the Kilifi Health and Demographic Surveillance System (KHDSS): 2008-2015

BACKGROUND

Use of bednets reduces malaria morbidity and mortality. In Kilifi, Kenya, there was a mass distribution of free nets to children < 5 years in 2006. In 2009, a new policy was implemented to offer bednets to pregnant women and children < 5 years free of charge. Nets were again distributed to children and adults through national mass campaigns in 2012 and 2015. We aimed to evaluate trends in bednet ownership and usage, and the effect of bednets on the incidence of malaria hospitalization in children < 5 years within the Kilifi Health and Demographic Surveillance System (KHDSS).

METHODS

Bednet ownership and usage were assessed during eight routine enumeration rounds of the KHDSS between 2008 and 2015. Malaria admissions (i.e. admissions to hospital with P. falciparum > 2500 parasitemia per μl) among children < 5 years were captured using a system of continuous vital registration that links admissions at Kilifi County Hospital to the KHDSS population register. Survival analysis was used to assess relative risk of hospitalization with malaria among children that reported using a bednet compared to those who did not.

RESULTS

We observed 63% and 62% mean bednet ownership and usage, respectively, over the eight-survey period. Among children < 5 years, reported bednet ownership in October-December 2008 was 69% and in March-August 2009 was 73% (p < 0.001). An increase was also observed following the mass distribution campaigns in 2012 (62% in May-July 2012 vs 90% in May-October 2013, p < 0.001) and 2015 (68% in June-September 2015 vs 93% in October-November 2015, p < 0.001). Among children <5 years who reported using a net the night prior to the survey, the incidence of malaria hospitalization per 1000 child-years was 2.91 compared to 4.37 among those who did not (HR = 0.67, 95% CI: 0.52, 0.85 [p = 0.001]).

CONCLUSION

On longitudinal surveillance, increasing bednet ownership and usage corresponded to mass distribution campaigns; however, this method of delivering bednets did not result in sustained improvements in coverage. Among children < 5 years old bednet use was associated with a 33% decreased incidence of malaria hospitalization.

Should First-line Empiric Treatment Strategies for Neonates Cover Coagulase-negative Staphylococcal Infections in Kenya?

BACKGROUND

Neonatal mortality remains high in sub-Saharan Africa, and a third of deaths are estimated to result from infection. While coagulase-negative staphylococci (CoNS) are leading neonatal pathogens in resource-rich settings, their role, and the need for early anti-Staphylococcal treatment in empiric antibiotic guidelines, is unknown in sub-Saharan Africa.

METHODS

We examined systematic clinical and microbiologic surveillance data from all neonatal admissions to Kilifi County Hospital (1998-2013) to determine associated case fatality and/or prolonged duration of admission associated with CoNS in neonates treated according to standard World Health Organization guidelines.

RESULTS

CoNS was isolated from blood culture in 995 of 9552 (10%) neonates. Case fatality among neonates with CoNS isolated from blood did not differ from other neonatal admissions (P = 0.2), and duration of admission was not prolonged [odds ratio (OR) = 0.9 (0.7-1.0), P = 0.040]. Neonates with CoNS were more likely to have convulsions [OR = 1.4 (1.0-1.8), P = 0.031] but less likely to have impaired consciousness or severe indrawing [OR = 0.8 (0.7-0.9), P = 0.025; OR = 0.9 (0.7-1.0), P = 0.065].

CONCLUSIONS

CoNS isolation in blood cultures at admission was not associated with adverse clinical outcomes in neonates treated according to standard World Health Organization guidelines for hospital care in this setting. There is no evidence that first-line antimicrobial treatment guidelines should be altered to increase cover for CoNS infections in neonates in this setting.

Young people's and stakeholders' perspectives of adolescent sexual risk behavior in Kilifi County, Kenya: A qualitative study

A lack of research exists around the most common forms of sexual risk behaviors among adolescents, including their underlying factors, in Sub-Saharan Africa. Using an Ecological Model of Adolescent Behavior, we explore the perceptions of 85 young people and 10 stakeholders on sexual risk behavior of adolescents in Kilifi County on the coast of Kenya. Our findings show that transactional sex, early sexual debut, coerced sex, and multiple sexual partnerships are prevalent. An urgent need exists to develop measures to counter sexual risk behaviors. The results contribute to understanding the range of risks and protective factors in differing contexts, tackling underlying issues at individual, family, local institutional, wider socio-economic, and political levels.

Micro-epidemiological structuring of Plasmodium falciparum parasite populations in regions with varying transmission intensities in Africa

Background: The first models of malaria transmission assumed a completely mixed and homogeneous population of parasites.  Recent models include spatial heterogeneity and variably mixed populations. However, there are few empiric estimates of parasite mixing with which to parametize such models.

Methods: Here we genotype 276 single nucleotide polymorphisms (SNPs) in 5199 P. falciparum isolates from two Kenyan sites (Kilifi county and Rachuonyo South district) and one Gambian site (Kombo coastal districts) to determine the spatio-temporal extent of parasite mixing, and use Principal Component Analysis (PCA) and linear regression to examine the relationship between genetic relatedness and distance in space and time for parasite pairs.

Results: Using 107, 177 and 82 SNPs that were successfully genotyped in 133, 1602, and 1034 parasite isolates from The Gambia, Kilifi and Rachuonyo South district, respectively, we show that there are no discrete geographically restricted parasite sub-populations, but instead we see a diffuse spatio-temporal structure to parasite genotypes.  Genetic relatedness of sample pairs is predicted by relatedness in space and time.

Conclusions: Our findings suggest that targeted malaria control will benefit the surrounding community, but unfortunately also that emerging drug resistance will spread rapidly through the population.

Micro-epidemiological structuring of Plasmodium falciparum parasite populations in regions with varying transmission intensities in Africa

Background: The first models of malaria transmission assumed a completely mixed and homogeneous population of parasites. Recent models include spatial heterogeneity and variably mixed populations. However, there are few empiric estimates of parasite mixing with which to parametize such models. Methods: Here we genotype 276 single nucleotide polymorphisms (SNPs) in 5199 P. falciparum isolates from two Kenyan sites (Kilifi county and Rachuonyo South district) and one Gambian site (Kombo coastal districts) to determine the spatio-temporal extent of parasite mixing, and use Principal Component Analysis (PCA) and linear regression to examine the relationship between genetic relatedness and distance in space and time for parasite pairs. Results: Using 107, 177 and 82 SNPs that were successfully genotyped in 133, 1602, and 1034 parasite isolates from The Gambia, Kilifi and Rachuonyo South district, respectively, we show that there are no discrete geographically restricted parasite sub-populations, but instead we see a diffuse spatio-temporal structure to parasite genotypes. Genetic relatedness of sample pairs is predicted by relatedness in space and time. Conclusions: Our findings suggest that targeted malaria control will benefit the surrounding community, but unfortunately also that emerging drug resistance will spread rapidly through the population.

Prevalence, risk factors, and neurobehavioral comorbidities of epilepsy in Kenyan children

Objective

To investigate the prevalence, risk factors, clinical features, and neurobehavioral comorbidities of epilepsy and acute symptomatic seizures in school‐aged children in Kilifi, Kenya.

Methods

Randomly selected children (N = 11,223) were screened for epilepsy and other neurodevelopmental disorders. Those who screened positive were invited for further clinical, electroencephalographic (EEG), and neuropsychological evaluations. Prevalence was measured by dividing cases by screened population, providing Agresti–Coull confidence intervals (CIs). Prevalence ratios were computed using log binomial regression, and odds ratios (ORs) were computed using logistic regression; both were implemented with generalized linear models. Attention‐deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD), and other neurodevelopmental impairments were assessed in cases and controls.

Results

Prevalence of lifetime epilepsy was 20.9 per 1,000 (95% CI = 18.4–23.7), and that of active epilepsy was 11.5 per 1,000 (95% CI = 9.7–13.6). Prevalence of acute symptomatic seizures was 68.8 per 1,000 (95% CI = 64.2–73.6). Acute symptomatic seizures preceded a diagnosis of epilepsy in 8% of children. Of 98 children diagnosed with epilepsy, focal seizures were seen in 79%, abnormal EEG was seen in 39%, and 83% were not receiving antiepileptic drugs. Childhood absence epilepsy and Lennox–Gastaut epilepsy were the most easily identifiable epilepsy syndromes. Perinatal complications, previous hospitalization, geophagia, and snoring were risk factors for epilepsy. Family history of seizures, abnormal pregnancy, previous hospitalization, and snoring were risk factors for acute symptomatic seizures. Neurobehavioral comorbidities were present in 54% of subjects with lifetime epilepsy and in 3% of controls, with associations for individual comorbidities being statistically significant: ADHD (OR = 14.55, 95% CI = 7.54–28.06), ASD (OR = 36.83, 95% CI = 7.97–170.14), and cognitive impairments (OR = 14.55, 95% CI = 3.52–60.14).

Significance

The burden of seizure disorders in this area is higher than in locations in high‐income countries, and can be reduced by preventing risk factors. A comprehensive management plan for neurobehavioral comorbidities of epilepsy should be incorporated into standard epilepsy care.

A growth reference for mid upper arm circumference for age among school age children and adolescents, and validation for mortality: growth curve construction and longitudinal cohort study

Objectives To construct growth curves for mid-upper-arm circumference (MUAC)-for-age z score for 5-19 year olds that accord with the World Health Organization growth standards, and to evaluate their discriminatory performance for subsequent mortality.Design Growth curve construction and longitudinal cohort study.Setting United States and international growth data, and cohorts in Kenya, Uganda, and Zimbabwe.Participants The Health Examination Survey (HES)/National Health and Nutrition Examination Survey (NHANES) US population datasets (age 5-25 years), which were used to construct the 2007 WHO growth reference for body mass index in this age group, were merged with an imputed dataset matching the distribution of the WHO 2006 growth standards age 2-6 years. Validation data were from 685 HIV infected children aged 5-17 years participating in the Antiretroviral Research for Watoto (ARROW) trial in Uganda and Zimbabwe; and 1741 children aged 5-13 years discharged from a rural Kenyan hospital (3.8% HIV infected). Both cohorts were followed-up for survival during one year.Main outcome measures Concordance with WHO 2006 growth standards at age 60 months and survival during one year according to MUAC-for-age and body mass index-for-age z scores.Results The new growth curves transitioned smoothly with WHO growth standards at age 5 years. MUAC-for-age z scores of -2 to -3 and less than-3, compared with -2 or more, was associated with hazard ratios for death within one year of 3.63 (95% confidence interval 0.90 to 14.7; P=0.07) and 11.1 (3.40 to 36.0; P<0.001), respectively, among ARROW trial participants; and 2.22 (1.01 to 4.9; P=0.04) and 5.15 (2.49 to 10.7; P<0.001), respectively, among Kenyan children after discharge from hospital. The AUCs for MUAC-for-age and body mass index-for-age z scores for discriminating subsequent mortality were 0.81 (95% confidence interval 0.70 to 0.92) and 0.75 (0.63 to 0.86) in the ARROW trial (absolute difference 0.06, 95% confidence interval -0.032 to 0.16; P=0.2) and 0.73 (0.65 to 0.80) and 0.58 (0.49 to 0.67), respectively, in Kenya (absolute difference in AUC 0.15, 0.07 to 0.23; P=0.0002).Conclusions The MUAC-for-age z score is at least as effective as the body mass index-for-age z score for assessing mortality risks associated with undernutrition among African school aged children and adolescents. MUAC can provide simplified screening and diagnosis within nutrition and HIV programmes, and in research.

Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya

Multidrug resistant (MDR) Klebsiella pneumoniae is a common cause of nosocomial infections worldwide. Recent years have seen an explosion of resistance to extended-spectrum β-lactamases (ESBLs) and emergence of carbapenem resistance. Here, we examine 198 invasive K. pneumoniae isolates collected from over a decade in Kilifi County Hospital (KCH) in Kenya. We observe a significant increase in MDR K. pneumoniae isolates, particularly to third generation cephalosporins conferred by ESBLs. Using whole-genome sequences, we describe the population structure and the distribution of antimicrobial resistance genes within it. More than half of the isolates examined in this study were ESBL-positive, encoding CTX-M-15, SHV-2, SHV-12 and SHV-27, and 79% were MDR conferring resistance to at least three antimicrobial classes. Although no isolates in our dataset were found to be resistant to carbapenems we did find a plasmid with the genetic architecture of a known New Delhi metallo-β-lactamase-1 (NDM)-carrying plasmid in 25 isolates. In the absence of carbapenem use in KCH and because of the instability of the NDM-1 gene in the plasmid, the NDM-1 gene has been lost in these isolates. Our data suggests that isolates that encode NDM-1 could be present in the population; should carbapenems be introduced as treatment in public hospitals in Kenya, resistance is likely to ensue rapidly.

Linking health facility data from young adults aged 18-24 years to longitudinal demographic data: Experience from The Kilifi Health and Demographic Surveillance System

Background: In 2014, a pilot study was conducted to test the feasibility of linking clinic attendance data for young adults at two health facilities to the population register of the Kilifi Health and Demographic Surveillance System (KHDSS). This was part of a cross-sectional survey of health problems of young people, and we tested the feasibility of using the KHDSS platform for the monitoring of future interventions. Methods: Two facilities were used for this study. Clinical data from consenting participants aged 18-24 years were matched to KHDSS records. Data matching was achieved using national identity card numbers or otherwise using a matching algorithm based on names, sex, date of birth, location of residence and the names of other homestead members. A study form was administered to all matched patients to capture reasons for their visits and time taken to access the services. Distance to health facility from a participants’ homestead was also computed. Results: 628 participated in the study: 386 (61%) at Matsangoni Health Centre, and 242 (39%) at Pingilikani Dispensary. 610 (97%) records were matched to the KHDSS register. Most records (605; 96%) were matched within these health facilities, while 5 (1%) were matched during homestead follow-up visits.  463 (75.9%) of those matched were women. Antenatal care (25%), family planning (13%), respiratory infections (9%) and malaria (9%) were the main reasons for seeking care. Antenatal clinic visits (n=175) and malaria (n=27) were the commonest reasons among women and men, respectively. Participants took 1-1.5 hours to access the services; 490 (81.0%) participants lived within 5 kilometres of a facility. Conclusions: With a full-time research clerk at each health facility, linking health-facility attendance data to a longitudinal HDSS platform was feasible and could be used to monitor and evaluate the impact of health interventions on health care outcomes among young people.

Sustained reduction in vaccine-type invasive pneumococcal disease despite waning effects of a catch-up campaign in Kilifi, Kenya: A mathematical model based on pre-vaccination data

•

We predict a substantial decline in the carriage prevalence of vaccine serotypes.

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About a 56% reduction in invasive pneumococcal disease is also predicted.

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The decline is predicted to be sustainable ten years post-vaccination.

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The current vaccination schedule is unlikely to achieve elimination of vaccine serotypes.

Background

In 2011, Kenya introduced the 10-valent pneumococcal conjugate vaccine together with a catch-up campaign for children aged <5 years in Kilifi County. In a post-vaccination surveillance study based in Kilifi, there was a substantial decline in invasive pneumococcal disease (IPD). However, given the continued circulation of the vaccine serotypes it is possible that vaccine-serotype disease may re-emerge once the effects of the catch-up campaign wear off.

Methods

We developed a compartmental, age-structured dynamic model of pneumococcal carriage and invasive disease for three serotype groups: the 10-valent vaccine serotypes and two groups of non-vaccine serotypes based on their susceptibility to mutual competition. The model was calibrated to age- and serotype-specific data on carriage and IPD in the pre-vaccination era and used to predict carriage prevalence and IPD up to ten years post-vaccination in Kilifi. The model was validated against the observed carriage prevalence after vaccine introduction.

Results

The model predicts a sustained reduction in vaccine-type pneumococcal carriage prevalence from 33% to 8% in infants and from 30% to 8% in 1–5 year olds over the 10-year period following vaccine introduction. The incidence of IPD is predicted to decline across all age groups resulting in an overall reduction of 56% in the population, corresponding to 10.4 cases per 100,000 per year. The vaccine-type IPD incidence is estimated to decline by 83% while non-vaccine-type IPD incidence is predicted to increase by 52%. The model's predictions of carriage prevalence agrees well with the observed data in the first five years post-vaccination.

Conclusion

We predict a sustained and substantial decline in IPD through PCV vaccination and that the current regimen is insufficient to fully eliminate vaccine-serotype circulation in the model. We show that the observed impact is likely to be sustained despite waning effects of the catch-up campaign.

Assessing the efficiency of catch-up campaigns for the introduction of pneumococcal conjugate vaccine: a modelling study based on data from PCV10 introduction in Kilifi, Kenya

BACKGROUND

The World Health Organisation recommends the use of catch-up campaigns as part of the introduction of pneumococcal conjugate vaccines (PCVs) to accelerate herd protection and hence PCV impact. The value of a catch-up campaign is a trade-off between the costs of vaccinating additional age groups and the benefit of additional direct and indirect protection. There is a paucity of observational data, particularly from low- and middle-income countries, to quantify the optimal breadth of such catch-up campaigns.

METHODS

In Kilifi, Kenya, PCV10 was introduced in 2011 using the three-dose Expanded Programme on Immunisation infant schedule and a catch-up campaign in children <5 years old. We fitted a transmission dynamic model to detailed local data, including nasopharyngeal carriage and invasive pneumococcal disease (IPD), to infer the marginal impact of the PCV catch-up campaign over hypothetical routine cohort vaccination in that setting and to estimate the likely impact of alternative campaigns and their dose efficiency.

RESULTS

We estimated that, within 10 years of introduction, the catch-up campaign among children <5 years old prevents an additional 65 (48-84) IPD cases across age groups, compared to PCV cohort introduction alone. Vaccination without any catch-up campaign prevented 155 (121-193) IPD cases and used 1321 (1058-1698) PCV doses per IPD case prevented. In the years after implementation, the PCV programme gradually accrues herd protection, and hence its dose efficiency increases: 10 years after the start of cohort vaccination alone the programme used 910 (732-1184) doses per IPD case averted. We estimated that a two-dose catch-up among children <1 year old uses an additional 910 (732-1184) doses per additional IPD case averted. Furthermore, by extending a single-dose catch-up campaign to children aged 1 to <2 years and subsequently to those aged 2 to <5 years, the campaign uses an additional 412 (296-606) and 543 (403-763) doses per additional IPD case averted. These results were not sensitive to vaccine coverage, serotype competition, the duration of vaccine protection or the relative protection of infants.

CONCLUSIONS

We find that catch-up campaigns are a highly dose-efficient way to accelerate population protection against pneumococcal disease.

Gendered negotiations for research participation in community-based studies: implications for health research policy and practice

There is a growing literature documenting the complex realities of consent processes in the field, and the negotiations and ethical dilemmas involved. Much has also been written about how gender and power shape household decision-making processes. However, these bodies of literature have rarely been brought together to inform research theory and practice in low-income settings. In this paper, qualitative research (observation, focus group discussions and interviews) were used alongside large clinical community-based studies conducted on the Kenyan Coast to explore how gender and power relations within households and communities and between fieldworkers and communities shape consent processes and interactions. This exploration is embedded in relevant literature and the implications for community-based health research policy and practice are considered. Across diverse forms of households, we observed significant consultation on whether or not to participate in research. Although men are typically described as household decision-makers, in practice, decision-making processes are often far more nuanced, with many women using their agency to control, sometimes subtly, the decisions made. Where decisions are made without adequately consulting women, many find strategies to exercise their choice, in ways that safeguard important relationships within households in the longer term. We also found that the gender of field staff who typically conduct research activities in the field, including consent processes, can influence household dynamics and decision-making processes with important implications for the science and ethics of research. It is essential that frontline field staff and their supervisors are aware of the complex and gendered realities of consent processes at household level, and their implications, and that they develop appropriate context-informed approaches that support ethical practice.

Mortality after Inpatient Treatment for Severe Pneumonia in Children: a Cohort Study

BACKGROUND

Although pneumonia is a leading cause of inpatient mortality, deaths may also occur after discharge from hospital. However, prior studies have been small, in selected groups or did not fully evaluate risk factors, particularly malnutrition and HIV. We determined 1-year post-discharge mortality and risk factors among children diagnosed with severe pneumonia.

METHODS

A cohort study of children aged 1-59 months admitted to Kilifi County Hospital with severe pneumonia (2007-12). The primary outcome was death <1 year after discharge, determined through Kilifi Health and Demographic Surveillance System (KHDSS) quarterly census rounds.

RESULTS

Of 4184 children (median age 9 months) admitted with severe pneumonia, 1041 (25%) had severe acute malnutrition (SAM), 267 (6.4%) had a positive HIV antibody test, and 364 (8.7%) died in hospital. After discharge, 2279 KHDSS-resident children were followed up; 70 (3.1%) died during 2163 child-years: 32 (95% confidence interval (CI) 26, 41) deaths per 1000 child years. Post-discharge mortality was greater after admission for severe pneumonia than for other diagnoses, hazard ratio 2.5 (95% CI 1.2, 5.3). Malnutrition, HIV status, age and prolonged hospitalisation, but not signs of pneumonia severity, were associated with post-discharge mortality. Fifty-two per cent (95% CI 37%, 63%) of post-discharge deaths were attributable to low mid-upper arm circumference and 11% (95% CI 3.3%, 18%) to a positive HIV test.

CONCLUSIONS

Admission with severe pneumonia is an important marker of vulnerability. Risk stratification and better understanding of the mechanisms underlying post-discharge mortality, especially for undernourished children, are needed to reduce mortality after treatment for pneumonia.

Health service provision for people with epilepsy in sub-Saharan Africa: A situational review

BACKGROUND

Epilepsy is a public health issue in sub-Saharan Africa (SSA) where many people with the condition receive no treatment. Health-care services for epilepsy in this region have not been comprehensively assessed. We examined key features of epilepsy health services provided in SSA.

METHODOLOGY

This was a scoping review conducted using pre-specified protocols. We implemented an electronic search strategy to identify relevant citations using PUBMED, EMBASE, Web of Science, Scopus, Cumulative Index to Nursing and Allied Health Literature (CINAHL), African Index Medicus (AIM), Open Grey, Cochrane database, and Google Scholar. Articles eligible for full-text review were screened and data of interest were reported.

RESULT

The search identified 81 eligible articles, forty-nine from East Africa, 19 from West Africa, 8 from South Africa, and 5 from Central Africa. A variety of care services were identified, with reporting of rural epilepsy care in 75% of retrieved articles mainly from East and South African countries. The majority of the rural epilepsy clinics were health worker- or nurse-led, reporting good seizure control in about two-thirds of patients using phenobarbital as the most commonly prescribed antiepileptic drug. Funding for rural epilepsy care came mainly from external donor agencies.

CONCLUSION

We attempted to provide a 'snapshot' of epilepsy care services in SSA. The successes achieved in some of the centers are due to the use of existing primary health-care systems and employing non-physician health-care personnel. The true picture of epilepsy care coverage is not apparent due to the lack of data and proper health system structure in most parts of SSA. As more individuals begin to receive care, the long-term funding for epilepsy care in African countries will depend on the commitment of their respective governments.

An overview of mental health care system in Kilifi, Kenya: results from an initial assessment using the World Health Organization's Assessment Instrument for Mental Health Systems

Background

Little is known about the state of mental health systems in Kenya. In 2010, Kenya promulgated a new constitution, which devolved national government and the national health system to 47 counties including Kilifi County. There is need to provide evidence from mental health systems research to identify priority areas in Kilifi’s mental health system for informing county health sector decision making. We conducted an initial assessment of state of mental health systems in Kilifi County and documented resources, policy and legislation and spectrum of mental, neurological and substance use disorders.

Methods

This was a pilot study that used the brief version of the World Health Organization’s Assessment Instrument for Mental Health Systems Version 2.2 to collect data. Data collection was based on the year 2014.

Results

Kilifi county has two public psychiatric outpatient units that are part of general hospitals. There is no standalone mental hospital in Kilifi. There are no inpatients or community based facilities for people with mental health problems. Although the psychiatric facilities in Kilifi have an essential drugs list, supply of drugs is erratic with frequent shortages. There is no psychiatrist or psychologist in Kilifi with only two psychiatric nurses for a population of approximately 1.2 million people. Schizophrenia was the commonest reason for visiting outpatient facilities (47.1%) while suicidal ideation was the least common (0.4%). Kenya’s mental health policy, which is being used by Kilifi County, is outdated and does not cater for the current mental health needs of Kilifi. There is no specific legislation to protect the rights of people with mental health problems. No budget exists specifically for mental health care. There have been no efforts to integrate mental health care into primary care in Kilifi, and there is no empirical research work to evaluate its feasibility.

Conclusion

There is an urgent need to increase resources allocated for mental health in particular infrastructure and human resource. Policy and legislations need to be established to protect the rights of people with mental illnesses, and mental health should be integrated with primary care to increase access to services.

High prevalence of curable sexually transmitted infections among pregnant women in a rural county hospital in Kilifi, Kenya

BACKGROUND

Women attending antenatal care (ANC) in resource-limited countries are frequently screened for syphilis and HIV, but rarely for other sexually transmitted infections (STIs). We assessed the prevalence of curable STIs, defined as infection with either Chlamydia trachomatis or Neisseria gonorrhoeae or Trichomonas vaginalis, from July to September 2015.

METHODS

In a cross-sectional study, women attending ANC at the Kilifi County Hospital, Kenya, had a urine sample tested for C. trachomatis/N. gonorrhoeae by GeneXpert® and a vaginal swab for T. vaginalis by culture. Bacterial vaginosis (BV) was defined as a Nugent score of 7-10 of the Gram stain of a vaginal smear in combination with self-reported vaginal discharge. Genital ulcers were observed during collection of vaginal swabs. All women responded to questions on socio-demographics and sexual health and clinical symptoms of STIs. Predictors for curable STIs were assessed in multivariable logistic regression.

RESULTS

A total of 42/202 (20.8%, 95% confidence interval (CI):15.4-27.0) women had a curable STI. The prevalence was 14.9% for C. trachomatis (95% CI:10.2-20.5), 1.0% for N. gonorrhoeae (95% CI: 0.1-3.5), 7.4% for T. vaginalis (95% CI:4.2-12.0), 19.3% for BV (95% CI: 14.1-25.4) and 2.5% for genital ulcers (95% CI: 0.8-5.7). Predictors for infection with curable STIs included women with a genital ulcer (adjusted odds ratio (AOR) = 35.0, 95% CI: 2.7-461.6) compared to women without a genital ulcer, women who used water for cleaning after visiting the toilet compared to those who used toilet paper or other solid means (AOR = 4.1, 95% CI:1.5-11.3), women who reported having sexual debut ≤ 17 years compared to women having sexual debut ≥18 years (AOR = 2.7, 95% CI:1.1-6.6), and BV-positive women (AOR = 2.7, 95% CI:1.1-6.6) compared to BV-negative women.

CONCLUSION

One in five women attending ANC had a curable STI. These infections were associated with genital ulcers, hygiene practices, early sexual debut and bacterial vaginosis.

Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis

Detailed information on the source, spread and evolution of respiratory syncytial virus (RSV) during seasonal community outbreaks remains sparse. Molecular analyses of attachment (G) gene sequences from hospitalized cases suggest that multiple genotypes and variants co-circulate during epidemics and that RSV persistence over successive seasons is characterized by replacement and multiple new introductions of variants. No studies have defined the patterns of introduction, spread and evolution of RSV at the local community and household level. We present a whole genome sequence analysis of 131 RSV group A viruses collected during 6-month household-based RSV infection surveillance in Coastal Kenya, 2010 within an area of 12 km². RSV infections were identified by regular symptom-independent screening of all household members twice weekly. Phylogenetic analysis revealed that the RSV A viruses in nine households were closely related to genotype GA2 and fell within a single branch of the global phylogeny. Genomic analysis allowed the detection of household-specific variation in seven households. For comparison, using only G gene analysis, household-specific variation was found only in one of the nine households. Nucleotide changes were observed both intra-host (viruses identified from same individual in follow-up sampling) and inter-host (viruses identified from different household members) and these coupled with sampling dates enabled a partial reconstruction of the within household transmission chains. The genomic evolutionary rate for the household dataset was estimated as 2.307 × 10 ^− 3 (95% highest posterior density: 0.935–4.165× 10 ^− 3) substitutions/site/year. We conclude that (i) at the household level, most RSV infections arise from the introduction of a single virus variant followed by accumulation of household specific variation and (ii) analysis of complete virus genomes is crucial to better understand viral transmission in the community. A key question arising is whether prevention of RSV introduction or spread within the household by vaccinating key transmitting household members would lead to a reduced onward community-wide transmission.

Burden, risk factors, and comorbidities of behavioural and emotional problems in Kenyan children: a population-based study

BACKGROUND

Three-quarters of the burden of mental health problems occurs in low-and-middle-income countries, but few epidemiological studies of these problems in preschool children from sub-Saharan Africa have been published. Behavioural and emotional problems often start in early childhood, and this might be particularly important in Africa, where the incidence of perinatal and early risk factors is high. We therefore aimed to estimate the prevalence and risk factors of behavioural and emotional problems in young children in a rural area on the Kenyan coast.

METHODS

We did a population-based epidemiological study to assess the burden of behavioural and emotional problems in preschool children and comorbidities in the Kilifi Health and Demographic Surveillance System (KHDSS, a database formed of the population under routine surveillance linked to admissions to Kilifi County Hospital). We used the Child Behaviour Checklist (CBCL) to assess behavioural and emotional problems. We then determined risk factors and medical comorbidities associated with behavioural and emotional problems. The strength of associations between the risk factors and the behavioural and emotional problems was estimated using generalised linear models, with appropriate distribution and link functions.

FINDINGS

3539 families were randomly selected from the KHDSS. Of these, 3273 children were assessed with CBCL. The prevalence of total behavioural and emotional problems was 13% (95% CI 12-14), for externalising problems was 10% (9-11), and for internalising problems was 22% (21-24). The most common CBCL syndrome was somatic problems (21%, 20-23), whereas the most common DSM-IV-oriented scale was anxiety problems (13%, 12-14). Factors associated with total problems included consumption of cassava (risk ratio 5·68, 95% CI 3·22-10·03), perinatal complications (4·34, 3·21-5·81), seizure disorders (2·90, 2·24-3·77), and house status (0·11, 0·08-0·14). Seizure disorders, burn marks, and respiratory problems were important comorbidities of behavioural and emotional problems.

INTERPRETATION

Behavioural and emotional problems are common in preschool children in this Kenyan rural area and are associated with preventable risk factors. Behavioural and emotional problems and associated comorbidities should be identified and addressed in young children.

FUNDING

Wellcome Trust.

Clinical and Epidemiological Implications of 24-Hour Ambulatory Blood Pressure Monitoring for the Diagnosis of Hypertension in Kenyan Adults: A Population-Based Study

BACKGROUND

The clinical and epidemiological implications of using ambulatory blood pressure monitoring (ABPM) for the diagnosis of hypertension have not been studied at a population level in sub-Saharan Africa. We examined the impact of ABPM use among Kenyan adults.

METHODS AND RESULTS

We performed a nested case-control study of diagnostic accuracy. We selected an age-stratified random sample of 1248 adults from the list of residents of the Kilifi Health and Demographic Surveillance System in Kenya. All participants underwent a screening blood pressure (BP) measurement. All those with screening BP ≥140/90 mm Hg and a random subset of those with screening BP <140/90 mm Hg were invited to undergo ABPM. Based on the 2 tests, participants were categorized as sustained hypertensive, masked hypertensive, "white coat" hypertensive, or normotensive. Analyses were weighted by the probability of undergoing ABPM. Screening BP ≥140/90 mm Hg was present in 359 of 986 participants, translating to a crude population prevalence of 23.1% (95% CI 16.5-31.5%). Age standardized prevalence of screening BP ≥140/90 mm Hg was 26.5% (95% CI 19.3-35.6%). On ABPM, 186 of 415 participants were confirmed to be hypertensive, with crude prevalence of 15.6% (95% CI 9.4-23.1%) and age-standardized prevalence of 17.1% (95% CI 11.0-24.4%). Age-standardized prevalence of masked and white coat hypertension were 7.6% (95% CI 2.8-13.7%) and 3.8% (95% CI 1.7-6.1%), respectively. The sensitivity and specificity of screening BP measurements were 80% (95% CI 73-86%) and 84% (95% CI 79-88%), respectively. BP indices and validity measures showed strong age-related trends.

CONCLUSIONS

Screening BP measurement significantly overestimated hypertension prevalence while failing to identify ≈50% of true hypertension diagnosed by ABPM. Our findings suggest significant clinical and epidemiological benefits of ABPM use for diagnosing hypertension in Kenyan adults.

Predicting the relative impacts of maternal and neonatal respiratory syncytial virus (RSV) vaccine target product profiles: A consensus modelling approach

Background

Respiratory syncytial virus (RSV) is the major viral cause of infant and childhood lower respiratory tract disease worldwide. Defining the optimal target product profile (TPP) is complicated due to a wide range of possible vaccine properties, modalities and an incomplete understanding of the mechanism of natural immunity. We report consensus population level impact projections based on two mathematical models applied to a low income setting.

Method

Two structurally distinct age-specific deterministic compartmental models reflecting uncertainty associated with the natural history of infection and the mechanism by which immunity is acquired and lost were constructed. A wide range of vaccine TPPs were explored including dosing regime and uptake, and effects in the vaccinated individual on infectiousness, susceptibility, duration of protection, disease severity and interaction with maternal antibodies and natural induced immunity. These were combined with a range of vaccine implementation strategies, targeting the highest priority age group and calibrated using hospitalization data from Kilifi County Hospital, Kenya.

Findings

Both models were able to reproduce the data. The impact predicted by the two models was qualitatively similar across the range of TPPs, although one model consistently predicted higher impact than the other. For a proposed realistic range of scenarios of TPP combinations, the models predicted up to 70% reduction in hospitalizations in children under five years old. Vaccine designs which reduced the duration and infectiousness of infection were predicted to have higher impacts. The models were sensitive to the coverage and rate of loss of vaccine protection but not to the interaction between vaccine and maternal/naturally acquired immunity.

Conclusion

The results suggest that vaccine properties leading to reduced virus circulation by lessening the duration and infectiousness of infection upon challenge are of major importance in population RSV disease control. These features should be a focus for vaccine development.

Absence of Association between Cord Specific Antibody Levels and Severe Respiratory Syncytial Virus (RSV) Disease in Early Infants: A Case Control Study from Coastal Kenya

Background

The target group for severe respiratory syncytial virus (RSV) disease prevention is infants under 6 months of age. Vaccine boosting of antibody titres in pregnant mothers could protect these young infants from severe respiratory syncytial virus (RSV) associated disease. Quantifying protective levels of RSV-specific maternal antibody at birth would inform vaccine development.

Methods

A case control study nested in a birth cohort (2002–07) was conducted in Kilifi, Kenya; where 30 hospitalised cases of RSV-associated severe disease were matched to 60 controls. Participants had a cord blood and 2 subsequent 3-monthly blood samples assayed for RSV-specific neutralising antibody by the plaque reduction neutralisation test (PRNT). Two sample paired t test and conditional logistic regression were used in analyses of log₂PRNT titres.

Results

The mean RSV log₂PRNT titre at birth for cases and controls were not significantly different (P = 0.4) and remained so on age-stratification. Cord blood PRNT titres showed considerable overlap between cases and controls. The odds of RSV disease decreased with increase in log₂PRNT cord blood titre. There was a 30% reduction in RSV disease per unit increase in log₂PRNT titre (<3months age group) but not significant (P = 0.3).

Conclusions

From this study, there is no strong evidence of protection by maternal RSV specific antibodies from severe RSV disease. Cord antibody levels show wide variation with considerable overlap between cases and controls. It is likely that, there are additional factors to specific PRNT antibody levels which determine susceptibility to severe RSV disease. In addition, higher levels of neutralizing antibody beyond the normal range may be required for protection; which it is hoped can be achieved by a maternal RSV vaccine.

Invasive Group A Streptococcus Infection among Children, Rural Kenya

These infections cause serious illness, especially in neonates.

To determine the extent of group A Streptococcus (GAS) infections in sub-Saharan Africa and the serotypes that cause disease, we analyzed surveillance data for 64,741 hospital admissions in Kilifi, Kenya, during 1998–2011. We evaluated incidence, clinical presentations, and emm types that cause invasive GAS infection. We detected 370 cases; of the 369 for which we had data, most were skin and soft tissue infections (70%), severe pneumonia (23%), and primary bacteremia (14%). Overall case-fatality risk was 12%. Incidence of invasive GAS infection was 0.6 cases/1,000 live births among neonates, 101/100,000 person-years among children <1 year of age, and 35/100,000 among children <5 years of age. Genome sequencing identified 88 emm types. GAS causes serious disease in children in rural Kenya, especially neonates, and the causative organisms have considerable genotypic diversity. Benefit from the most advanced GAS type–specific vaccines may be limited, and efforts must be directed to protect against disease in regions of high incidence.

Sodium Disturbances in Children Admitted to a Kenyan Hospital: Magnitude, Outcome and Associated Factors

Background

Perturbations of blood sodium are the most frequently encountered electrolyte disorder in sick children, and may influence fluid therapy. We examined the frequency of blood sodium perturbations, and factors and outcomes associated with hyponatremia in children admitted to a rural Kenyan hospital and investigated the risk factors associated with deaths in hyponatremic children.

Methods

Plasma sodium levels and other laboratory parameters were measured in children admitted to a rural Kenyan hospital. Clinical measurements were collected using standard forms and entered into a computer database. The proportion of children admitted with hyponatremia was determined. Logistic regression models were used to investigate factors associated with hyponatremia, and death in those with hyponatremia.

Results

Abnormal plasma sodium occurred in 46.6% (95% confidence interval (95%CI) 43.5–49.6%) of 1026 pediatric admissions. Hyponatremia occurred in 44.4% (95%CI 41.4–47.5%) and hypernatremia in 2.1% (95%CI 1.3–3.0%). Malaria (40.8%) was the most common underlying primary diagnosis in hyponatremic children. Malaria, hyperglycemia, wasting, high creatinine levels and preserved consciousness were associated with hyponatremia. Pallor and seizures were associated with increased mortality in hyponatremic children.

Conclusions

Sodium disturbances are common in pediatric admissions to a County hospital in rural Kenya. Seizures and pallor were predictors of mortality in hyponatremic children.

Risk of convulsive epilepsy following acute seizures in Kenyan children

Objective

The prevalence of epilepsy is high in Africa, and people with epilepsy often have a history of acute seizures. We determined whether acute seizures are associated with risk for epilepsy in rural Africa, where both conditions are common and may have shared risk factors.

Methods

A total of 16,438 children (2,991 with acute seizures and 13,447 without seizures) admitted to Kilifi County Hospital from 2002 to 2008 were followed up with epidemiological surveys conducted in 2003 and 2008 to assess the prevalence of epilepsy and the associated risk factors. Cox proportional hazards regression models were used to identify the risk factors. Prevalence ratios were computed using log binomial regression models.

Results

The prevalence of epilepsy was higher in admissions with acute seizures (5.0% [95% confidence interval (CI), 4.3–5.9%]) than in those without seizures (0.7% [95% CI, 0.5–0.8%]), p < 0.0001). Acute seizures were associated with epilepsy after accounting for potential confounders in a Cox regression model (hazard ratio [HR] = 1.53 [95% CI, 1.10–2.14]). Prevalence was greater in complex acute seizures (5.9%; prevalence ratio [PR] = 1.58 [95% CI, 1.13–2.20]) or status epilepticus (7.5%; PR = 1.96 [95% CI, 1.32–2.91]) than in simple acute seizures (3.7%). Factors independently associated with epilepsy following acute seizures in Cox regression models were perinatal complications (HR = 3.60 [95% CI, 1.89–6.87]), cerebral palsy (HR = 1491.51 [95% CI, 144.30–15,416.21]), duration of follow‐up (HR = 1.21 [95% CI, 1.09–1.35]), and malnutrition (relative risk [RR] = 0.24 [95% CI, 0.08–0.69]).

Significance

Acute seizures in children are associated with subsequent risk for epilepsy that is greater than in the general population. The burden of epilepsy may be reduced by control of causes of acute seizures.

Human metapneumovirus epidemiological and evolutionary patterns in Coastal Kenya, 2007-11

BACKGROUND

Human metapneumovirus (HMPV) is an important global cause of severe acute respiratory infections in young children and the elderly. The epidemiology of HMPV in sub-Saharan Africa is poorly described and factors that allow its recurrent epidemics in communities not understood.

METHODS

We undertook paediatric inpatient surveillance for HMPV in Kilifi County Hospital (KCH) of Coastal Kenya between 2007 and 2011. Nasopharyngeal samples collected from children aged 1 day-59 months admitted with severe or very severe pneumonia, were tested for HMPV using real-time polymerase chain reaction (RT-PCR). Partial nucleotide sequences of the attachment (G) and fusion (F) surface proteins of positive samples were determined and phylogenetically analyzed.

RESULTS

HMPV was detected in 4.8 % (160/3320) of children [73.8 % (118/160) of these less than one year of age], ranging between 2.9 and 8.8 % each year over the 5 years of study. HMPV infections were seasonal in occurrence, with cases predominant in the months of November through April. These months frequently coincided with low rainfall, high temperature and low relative humidity in the location. Phylogenetic analysis of partial F and G sequences revealed three subgroups of HMPV, A2 (74 %, 91/123), B1 (3.2 %, 4/123) and B2 (22.8 %, 28/123) in circulation, with subgroup A2 predominant in majority of the epidemic seasons. Comparison of G sequences (local and global) provided a greater phylogenetic resolution over comparison of F sequences and indicated presence of probable multiple G antigenic variants within the subgroups due to differences in amino acid sequence, encoded protein length and glycosylation patterns.

CONCLUSION

The present study reveals HMPV is an important seasonal contributor to respiratory disease hospitalization in coastal Kenya, with an evolutionary pattern closely relating to that of respiratory syncytial virus.

Quantifying social contacts in a household setting of rural Kenya using wearable proximity sensors

Close proximity interactions between individuals influence how infections spread. Quantifying close contacts in developing world settings, where such data is sparse yet disease burden is high, can provide insights into the design of intervention strategies such as vaccination. Recent technological advances have enabled collection of time-resolved face-to-face human contact data using radio frequency proximity sensors. The acceptability and practicalities of using proximity devices within the developing country setting have not been investigated. We present and analyse data arising from a prospective study of 5 households in rural Kenya, followed through 3 consecutive days. Pre-study focus group discussions with key community groups were held. All residents of selected households carried wearable proximity sensors to collect data on their close (<1.5 metres) interactions. Data collection for residents of three of the 5 households was contemporaneous. Contact matrices and temporal networks for 75 individuals are defined and mixing patterns by age and time of day in household contacts determined. Our study demonstrates the stability of numbers and durations of contacts across days. The contact durations followed a broad distribution consistent with data from other settings. Contacts within households occur mainly among children and between children and adults, and are characterised by daily regular peaks in the morning, midday and evening. Inter-household contacts are between adults and more sporadic when measured over several days. Community feedback indicated privacy as a major concern especially regarding perceptions of non-participants, and that community acceptability required thorough explanation of study tools and procedures. Our results show for a low resource setting how wearable proximity sensors can be used to objectively collect high-resolution temporal data without direct supervision. The methodology appears acceptable in this population following adequate community engagement on study procedures. A target for future investigation is to determine the difference in contact networks within versus between households. We suggest that the results from this study may be used in the design of future studies using similar electronic devices targeting communities, including households and schools, in the developing world context.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (doi:10.1140/epjds/s13688-016-0084-2) contains supplementary material.

Age, Spatial, and Temporal Variations in Hospital Admissions with Malaria in Kilifi County, Kenya: A 25-Year Longitudinal Observational Study

BACKGROUND

Encouraging progress has been seen with reductions in Plasmodium falciparum malaria transmission in some parts of Africa. Reduced transmission might lead to increasing susceptibility to malaria among older children due to lower acquired immunity, and this has implications for ongoing control strategies.

METHODS AND FINDINGS

We conducted a longitudinal observational study of children admitted to Kilifi County Hospital in Kenya and linked it to data on residence and insecticide-treated net (ITN) use. This included data from 69,104 children aged from 3 mo to 13 y admitted to Kilifi County Hospital between 1 January 1990 and 31 December 2014. The variation in malaria slide positivity among admissions was examined in logistic regression models using the following predictors: location of the residence, calendar time, the child's age, ITN use, and the enhanced vegetation index (a proxy for soil moisture). The proportion of malaria slide-positive admissions declined from 0.56 (95% confidence interval [CI] 0.54-0.58) in 1998 to 0.07 (95% CI 0.06-0.08) in 2009 but then increased again through to 0.24 (95% CI 0.22-0.25) in 2014. Older children accounted for most of the increase after 2009 (0.035 [95% CI 0.030-0.040] among young children compared to 0.22 [95% CI 0.21-0.23] in older children). There was a nonlinear relationship between malaria risk and prevalence of ITN use within a 2 km radius of an admitted child's residence such that the predicted malaria positive fraction varied from ~0.4 to <0.1 as the prevalence of ITN use varied from 20% to 80%. In this observational analysis, we were unable to determine the cause of the decline in malaria between 1998 and 2009, which pre-dated the dramatic scale-up in ITN distribution and use.

CONCLUSION

Following a period of reduced transmission, a cohort of older children emerged who have increased susceptibility to malaria. Further reductions in malaria transmission are needed to mitigate the increasing burden among older children, and universal ITN coverage is a promising strategy to achieve this goal.

Human capital on the move: Education as a determinant of internal migration in selected INDEPTH surveillance populations in Africa

BACKGROUND

Education, as a key indicator of human capital, is considered one of the major determinants of internal migration, with previous studies suggesting that human capital accumulates in urban areas at the expense of rural areas. However, there is fragmentary evidence concerning the educational correlates of internal migration in sub-Saharan Africa.

OBJECTIVES

The study questions whether more precise measures of migration in Health and Demographic Surveillance System (HDSS) populations support the hypothesis that migrants are self-selected on human capital and more educated people are more likely to leave rural areas or enter urban areas within a geographical region.

METHODS

Using unique longitudinal data representing approximately 900,000 people living in eight sub-Saharan African HDSS sites that are members of the INDEPTH Network, the paper uses Event History Analysis techniques to examine the relationship between formal educational attainment and in-and out-migration, over the period 2009 to 2011.

RESULTS

Between 7% and 27% of these local populations are moving in or out of the HDSS area over this period. Education is positively associated with both in-and out-migration in the Kenyan HDSS areas; however, the education effect has no clear pattern in the HDSS sites in Burkina Faso, Mozambique, and South Africa.

CONCLUSIONS

Empirical results presented in this paper confirm a strong age profile of migration consistent with human capital expectation, yet the results point to variability in the association of education and the propensity to migrate. In particular, the hypothesis of a shift of human capital from rural to urban areas is not universally valid.

Maternal colonization with Streptococcus agalactiae and associated stillbirth and neonatal disease in coastal Kenya

Streptococcus agalactiae (group B streptococcus, GBS) causes neonatal disease and stillbirth, but its burden in sub-Saharan Africa is uncertain. We assessed maternal recto-vaginal GBS colonization (7,967 women), stillbirth and neonatal disease. Whole-genome sequencing was used to determine serotypes, sequence types and phylogeny. We found low maternal GBS colonization prevalence (934/7,967, 12%), but comparatively high incidence of GBS-associated stillbirth and early onset neonatal disease (EOD) in hospital (0.91 (0.25-2.3)/1,000 births and 0.76 (0.25-1.77)/1,000 live births, respectively). However, using a population denominator, EOD incidence was considerably reduced (0.13 (0.07-0.21)/1,000 live births). Treated cases of EOD had very high case fatality (17/36, 47%), especially within 24 h of birth, making under-ascertainment of community-born cases highly likely, both here and in similar facility-based studies. Maternal GBS colonization was less common in women with low socio-economic status, HIV infection and undernutrition, but when GBS-colonized, they were more probably colonized by the most virulent clone, CC17. CC17 accounted for 267/915 (29%) of maternal colonizing (265/267 (99%) serotype III; 2/267 (0.7%) serotype IV) and 51/73 (70%) of neonatal disease cases (all serotype III). Trivalent (Ia/II/III) and pentavalent (Ia/Ib/II/III/V) vaccines would cover 71/73 (97%) and 72/73 (99%) of disease-causing serotypes, respectively. Serotype IV should be considered for inclusion, with evidence of capsular switching in CC17 strains.

Comparison of allele frequencies of Plasmodium falciparum merozoite antigens in malaria infections sampled in different years in a Kenyan population

Background

Plasmodium falciparum merozoite antigens elicit antibody responses in malaria-endemic populations, some of which are clinically protective, which is one of the reasons why merozoite antigens are the focus of malaria vaccine development efforts. Polymorphisms in several merozoite antigen-encoding genes are thought to arise as a result of selection by the human immune system.

Methods

The allele frequency distribution of 15 merozoite antigens over a two-year period, 2007 and 2008, was examined in parasites obtained from children with uncomplicated malaria. In the same population, allele frequency changes pre- and post-anti-malarial treatment were also examined. Any gene which showed a significant shift in allele frequencies was also assessed longitudinally in asymptomatic and complicated malaria infections.

Results

Fluctuating allele frequencies were identified in codons 147 and 148 of reticulocyte-binding homologue (Rh) 5, with a shift from HD to YH haplotypes over the two-year period in uncomplicated malaria infections. However, in both the asymptomatic and complicated malaria infections YH was the dominant and stable haplotype over the two-year and ten-year periods, respectively. A logistic regression analysis of all three malaria infection populations between 2007 and 2009 revealed, that the chance of being infected with the HD haplotype decreased with time from 2007 to 2009 and increased in the uncomplicated and asymptomatic infections.

Conclusion

Rh5 codons 147 and 148 showed heterogeneity at both an individual and population level and may be under some degree of immune selection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-016-1304-8) contains supplementary material, which is available to authorized users.